Plugged Secondary Heat Exchanger – Symptoms & How to Clean it?

A secondary heat exchanger is part of any high-efficiency furnace – one with an AFUE efficiency rating of 90% or greater. After the super-hot gases pass out of the primary heat exchanger, they enter the secondary heat exchanger where even more heat is transferred out of the combustion gases before it leaves the flue and is lost.

This type of furnace is also considered a condensing furnace, since the exhaust leaves the primary heat exchanger and then travels to the secondary heat exchanger. At this point more heat is released and water vapor begins to form. That is important to note – water drops form in the secondary heat exchanger because the gases cool, and the moisture vapor condenses. Water provides a clue to a potential plugged secondary heat exchanger.

In this article you will learn about what happens if your secondary heat exchanger becomes plugged. We will also discuss the signs of a plugged secondary heat exchanger and what you need to do to fix the problem.

What are the Signs of a Plugged Secondary Heat Exchanger?

A blocked secondary heat exchanger isn’t common, but veteran furnace technicians see a few from year to year. It is important to spot the signs that may indicate that your secondary heat exchanger is plugged:

1. The condensate in your condensate drain pan is brown or black.

The dirty drain pan is a sign that the condensate is carrying unwanted debris to the drain pain. The common culprit is either soot or corroded polypropylene. In very old furnaces, that should probably be replaced anyway, the debris might be corrosion caused by acidic condensate.

2. Your carbon monoxide alarm goes off

This might be because a blockage in the heat exchanger is causing combustion gases to back up into the furnace, and they might escape into the air in your home. Those gases contain poisonous carbon monoxide.

Safety Note: The CO alarm going off might also indicate that you have a failed or cracked heat exchanger.

3. A Pungent Odor

This smell will most likely be a sulfur-like smell or burning rubber smell due to soot or corroded polypropylene in the tubes of the blocked secondary heat exchanger. You might notice this odor leaking inside your home near the furnace – if the heat exchanger is significantly blocked. To confirm the issue, find where your furnace exhaust is vented outside through a wall. Run the furnace and check the exhaust there. If the odor is strong – the exhaust might also be hazy or smoky rather than clear – this is a good indication that the heat exchanger has become blocked or clogged with soot or with pieces of the lining, a problem explained in the next section.

4. Water Leaking from the Furnace

Leaking water is a sign of several furnace issues, and a plugged heat exchanger is one of them. Condensate forms in the system as exhaust gases cool. Normally, the condensate enters a drain, and you never see it. If the water is leaking, it could be that the secondary heat exchanger is plugged, preventing the condensate from getting to the drain, and it is leaking out wherever it finds an exit.

What Causes the Plugged Secondary Heat Exchanger?

Technicians usually find one or both of these issues when diagnosing a blocked secondary heat exchanger.

1. Lining Failure

The most common culprit for a clogged or plugged secondary heat exchanger is the polypropylene coating pulling away from the metal. This will eventually fully plug your exchanger.

2. Poor Combustion

Your furnace might not be burning gas thoroughly, or the air-to-fuel mixture might be off, making it run rich – too much fuel. These issues create more soot than usual. Soot will become trapped in the secondary heat exchanger, building up over time until the exhaust gases cannot get through it. When a furnace burns inefficiently, it wastes natural gas or propane, whichever it burns. So, while soot is building up to dangerous levels, the furnace will also be using more gas than normal. If you see a rise in your heating bills and notice any of the other signs, the wasted gas might be further indication of a plugged secondary heat exchanger.

Can a Secondary Heat Exchanger be Cleaned?

If your secondary heat exchanger is clogged or plugged then the situation must be remedied as soon as possible. The first question many ask is, “Can you unclog a clogged secondary heat exchanger?” Some can be. In this video, the HVAC technician demonstrates cleaning a Goodman gas furnace heat exchanger – and it is a hassle! 

The tech then shows a Carrier heat exchanger that is plugged and explains that due to its design, cleaning it either can’t be done or is more work than necessary compared with replacing it. Why would a homeowner pay a technician for several hours of cleaning a secondary heat exchanger when the cost of a new one is about the same? Go new in that case.

Even if the answer is “yes,” the process is kind of tricky. You can clean your secondary heat exchanger, but it is not an easy task.

Your best bet would be to contact a licensed HVAC technician to make a house call.

If you read Pick HVAC much, you know we give clear instructions for DIY when possible, but sometimes calling a furnace technician makes more sense. This is an issue that really should be fixed properly for the safety of your household and the efficient and durable performance of your gas furnace.

If you call a furnace contractor, you can expect to pay anywhere from $60 to $150 per hour for the technician’s time, and this is a job that takes 2-3 hours to do properly. If you are handy and very mechanically inclined, you can follow the steps listed below to clean your secondary heat exchanger (BEWARE…THERE ARE A LOT OF STEPS!).

How to Clean a Secondary Heat Exchanger

Pro Tip: Take pictures of the furnace before you start to dismantle it and along the way. These pictures will assist you when re-assembling it.

  1. Turn off the electric and gas to the furnace – the electricity can be turned off using the switch at the furnace or the circuit on the electric panel; the gas line should have a gas valve on it near the furnace, and it should be turned so that the handle is perpendicular to the gas line
  2. Label all the wires before you disconnect anything – and as suggested, take a picture of the wiring to help you reconnect it as it was
  3. Remove the control access door, and open the gas supply union
  4. Locate the gas supply line and disconnect it from the gas valve
  5. Disconnect the wires connected to the gas valve, and remove the burner box cover
  6. Disconnect the combustion air supply pipe
  7. Remove the burner box assembly – it should slide out after its fasteners are removed
  8. Inspect the burners and clean them, if necessary, with a stiff wire brush
  9. Remove the vent from the furnace blower
  10. Remove the vent blower and collector box
  11. Using a stiff wire brush with a flexible handle, remove the any loose scale from the heat exchanger at the flue and burner openings
  12. Use a ½” diameter brush to clean away any debris in the secondary exchanger
  13. Use a vacuum to remove any other scale or additional debris from the secondary heat exchanger
  14. Put everything back together step by step
  15. Turn the gas on
  16. Check for any gas leaks with soapy water – mix up a 3-to-1 solution of water and dish soap, and rub the mixture on the gas connection to see if bubbles form indicating a gas leak
  17. If the gas connection is tight and there are no bubbles, turn on power to the furnace, and fire it up

Another option is to use soap, water, and a brush to clean the secondary heat exchanger. Remove the parts that make up the heat exchanger, and give them a thorough cleaning.  Let the parts dry, and then put them back together.

These are basic steps that apply to most heat exchangers, though probably they’ll be a little different for some furnaces.

If the furnace doesn’t function properly or if the odor is still present after running the furnace for 10-15 minutes, shut it down, turn off power to the furnace, and contact a furnace technician. Feel free to use the Free Local Quotes phone number or tab/form on this page to be contacted to top furnace repair contractors in your area. They are prescreened to be licensed and insured, and there’s no obligation or cost on your part to get their input and free estimates on repairs.

Written by

Rene has worked 10 years in the HVAC field and now is the Senior Comfort Specialist for PICKHVAC. He holds an HVAC associate degree and EPA & R-410A Certifications.

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